Research workbench
Crystal structure of the murine norovirus NS6 protease (inactive C139A mutant) with a C-terminal extension to include residue P1 prime of NS7
Analyse Crystal structure of the murine norovirus NS6 protease (inactive C139A mutant)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X2V
- Type
- protein
- Length
- 714 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS6 protease
- UniProt
- A0FJD7, Q80J95
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 6 distinct chains · 3% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS6 protease | protein | 174 | 3% helix, 46% strand | A0FJD7 |
| B | NS6 protease | protein | 185 | 3% helix, 46% strand | A0FJD7 |
| C | NS6 protease | protein | 172 | 3% helix, 49% strand | A0FJD7 |
| D | NS6 protease | protein | 171 | 4% helix, 47% strand | A0FJD7 |
| E | NS6 protease | protein | 5 | 0% helix, 0% strand | Q80J95 |
| F | NS6 protease | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- IMD · Imidazole · additive · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.69 | 0.80 | 55 | empty |
| 2 | 182 | 0.67 | 0.86 | 44 | empty |
| 3 | 304 | 0.58 | 0.77 | 40 | empty |
| 4 | 131 | 0.46 | 0.78 | 26 | IMD |
| 5 | 75 | 0.40 | 0.78 | 15 | empty |
Interfaces
9 interfaces between chains.
- C–D · 924 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 916 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 592 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 494 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 373 Ų buried · 1 hydrogen bond · protein-protein
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0FJD7
- Every structure of UniProt Q80J95
- Elsewhere: RCSB PDB 4X2V · PDBe 4X2V · UniProt A0FJD7 · UniProt Q80J95
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